5 // Created by SarahsWork on 10/28/13.
6 // Copyright (c) 2013 Schloss Lab. All rights reserved.
9 #ifndef Mothur_sracommand_h
10 #define Mothur_sracommand_h
12 #include "command.hpp"
15 /**************************************************************************************************/
17 class SRACommand : public Command {
23 vector<string> setParameters();
24 string getCommandName() { return "sra"; }
25 string getCommandCategory() { return "Sequence Processing"; }
27 string getOutputPattern(string);
29 string getHelpString();
30 string getCitation() { return "http://www.mothur.org/wiki/sra"; }
31 string getDescription() { return "create a Sequence Read Archive / SRA"; }
34 void help() { m->mothurOut(getHelpString()); }
38 int tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
39 string sfffile, fastqfile, platform, outputDir, groupfile, file, oligosfile;
40 vector<string> outputNames;
42 int readFile(vector<string>&);
43 int parseSffFile(vector<string>&);
44 int parseFastqFile(vector<string>&);
48 /**************************************************************************************************/